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| Status |
Public on Aug 17, 2012 |
| Title |
Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function, in a pattern indicative of functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of sub-cellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs encoding membrane, synaptic and other proteins in both mouse and Drosophila cells, and Mbnls also contribute to protein secretion. These findings hold several new implications for DM pathogenesis.
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| Overall design |
To assess global functions of Muscleblind proteins, RNA-Seq was performed using WT and Mbnl1 KO brain, heart, and muscle (5 mice each). Additionally, C2C12 mouse myoblasts were depleted of Mbnl1, Mbnl2, or both. Subcellular fractionation experiments were performed to analyze mRNA localization following depletion of Mbnl1 and Mbnl2 in C2C12 mouse myoblasts, and following depletion of Mbnl in Drosophila S-2R+ cells. CLIP-Seq was also performed against Mbnl1 in mouse brain, heart, muscle, and C2C12 myoblasts. Finally, ribosome footprinting was performed with C2C12 mouse myoblasts that were depleted of Mbnl1, Mbnl2, or both.
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| Contributor(s) |
Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB |
| Citation(s) |
22901804 |
| Submission date |
Aug 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric T Wang |
| Organization name |
University of Florida
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platforms (4)
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| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (55)
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| Relations |
| BioProject |
PRJNA172014 |
| SRA |
SRP014709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39911_RAW.tar |
590.0 Kb |
(http)(custom) |
TAR (of BED) |
| GSE39911_fly_fractionation_RPKM.txt.gz |
246.7 Kb |
(ftp)(http) |
TXT |
| GSE39911_myoblast_RPKM.txt.gz |
444.3 Kb |
(ftp)(http) |
TXT |
| GSE39911_myoblast_fractionation_RPKM.txt.gz |
480.6 Kb |
(ftp)(http) |
TXT |
| GSE39911_myoblast_ribo_RPKM.txt.gz |
435.8 Kb |
(ftp)(http) |
TXT |
| GSE39911_tissue_RPKM.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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